PDB-3nda: Crystal structure of serpin from tick Ixodes ricinus

ID or keywords:

Entry

Database: PDB / ID: 3nda

Title

Crystal structure of serpin from tick Ixodes ricinus

Components

Serpin-2

Keywords

HYDROLASE INHIBITOR / serpin / vaccination target / tick

Function / homology

Function and homology information

immune system process / serine-type endopeptidase inhibitor activity / toxin activity / extracellular space
Similarity search - Function

Biological species

Ixodes ricinus (castor bean tick)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Rezacova, P. / Kovarova, Z. / Chmelar, J. / Mares, M.

Citation

Journal: Blood / Year: 2011
Title: A tick salivary protein targets cathepsin G and chymase and inhibits host inflammation and platelet aggregation.
Authors: Chmelar, J. / Oliveira, C.J. / Rezacova, P. / Francischetti, I.M. / Kovarova, Z. / Pejler, G. / Kopacek, P. / Ribeiro, J.M. / Mares, M. / Kopecky, J. / Kotsyfakis, M.

History

Deposition	Jun 7, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 27, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 11, 2013	Group: Database references
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3nda.cif.gz	258 KB	Display	PDBx/mmCIF format
PDB format	pdb3nda.ent.gz	199.8 KB	Display	PDB format
PDBx/mmJSON format	3nda.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nd/3nda ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3nda	HTTPS FTP

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Related structure data

Related structure data	1hleS S: Starting model for refinement
Similar structure data	2vdy-1 4c49-2 6hgi-d 2riv-d 2xn7-d 3eox-d 6hgk-d 5om8-d 5om5-d 2riw-d 4bb2-d 3q03-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#53 - May 2004 Serpins similarity (10)

Deposited unit

A: Serpin-2

B: Serpin-2

hetero molecules

84.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Serpin-2

defined by author&software
42.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Serpin-2

hetero molecules

defined by author&software
42.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.575, 84.575, 124.412
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

#1: Protein	Serpin-2 Mass: 42147.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Plasmid: pET-like / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q06B74
#2: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20mM HEPES pH 7.2, 0.075M MES pH 6.5, 9 % (w/v) PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.953 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953 Å / Relative weight: 1
Reflection	Resolution: 1.8→84.52 Å / Num. all: 80571 / Num. obs: 80249 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / B_iso Wilson estimate: 23.2 Å² / R_merge(I) obs: 0.046 / Net I/σ(I): 32.8
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.358 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7790 / % possible all: 97.3

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Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC	5.3.0037	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1HLE

1hle

Resolution: 1.8→30 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.947 / SU B: 5.16 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21222	4026	5 %	RANDOM
R_work	0.17073	-	-	-
obs	0.17283	76177	99.62 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 26.216 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.87 Å²	0 Å²	0 Å²
2-	-	-0.87 Å²	0 Å²
3-	-	-	1.73 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5898	0	16	875	6789

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	6281
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.22	1.967	8557
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.028	5	812
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.643	24.286	308
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.15	15	1109
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.724	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	973
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4809
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	3035
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	4323
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	790
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.168	0.2	91
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.123	0.2	67
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.562	1.5	3945
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.883	2	6239
X-RAY DIFFRACTION	r_scbond_it	1.59	3	2588
X-RAY DIFFRACTION	r_scangle_it	2.538	4.5	2283
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
1454	medium positional	0.35	0.5
1321	loose positional	0.66	5
1454	medium thermal	1.27	2
1321	loose thermal	1.7	10

LS refinement shell

Resolution: 1.802→1.849 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.315	285	-
R_work	0.247	5415	-
obs	-	-	96.38 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	6.2937	3.0823	0.1421	20.5744	3.0584	5.916	0.1293	-0.2228	0.563	0.3699	-0.2863	0.489	-0.5634	-0.5088	0.157	-0.059	0.046	0.0395	-0.0004	0.0081	-0.0037	13.479	32.125	3.62
2	1.1517	2.2236	-0.5586	4.2978	-1.0131	1.1827	-0.1641	0.2644	0.0907	-0.5164	0.2598	-0.145	0.0067	-0.1425	-0.0956	-0.0194	-0.0008	0.0667	0.0061	0.0199	-0.0027	19.268	22.133	-6.612
3	5.0889	1.2958	0.7153	3.1255	1.4288	4.742	-0.0836	0.3987	0.3028	-0.4488	0.126	0.0881	-0.5339	-0.3067	-0.0425	0.0269	0.0429	0.0476	-0.0103	0.0105	0.0073	17.229	34.732	-2.303
4	0.8516	-0.7041	0.3507	5.0735	-2.0489	1.2709	0.1276	0.0677	-0.0014	-0.0229	-0.0484	-0.1983	0.0887	0.0335	-0.0791	-0.0227	-0.0093	-0.0374	-0.038	-0.0417	0.0313	25.443	27.035	14.537
5	2.1686	0.7717	-0.9847	0.3231	-0.4415	0.6179	0.188	-0.0351	0.2543	0.1073	-0.057	0.1212	-0.1416	0.1147	-0.131	0.0141	-0.0004	0.1101	-0.0393	-0.0004	0.2109	35.081	34.427	-4.436
6	3.7737	2.3307	-3.5791	1.8182	-1.7513	3.9515	0.1003	-0.1091	0.0898	-0.01	-0.0327	0.162	-0.0774	0.1515	-0.0677	-0.0845	0.0209	-0.0031	0.0184	0.0364	0.1069	40.892	21.481	-3.25
7	2.2355	1.1135	-3.1672	1.5016	-1.9359	5.3045	0.0279	0.0383	0.1493	-0.0691	0.0034	-0.1763	0.0158	0.1482	-0.0313	-0.1171	-0.0015	-0.0231	-0.0445	0.0008	0.0423	30.651	16.91	1.557
8	1.4671	2.1572	5.0044	8.6791	5.1582	27.5442	0.0861	-0.1259	-0.1306	0.1043	-0.1917	-0.3997	0.8678	0.2571	0.1056	0.0316	0.0413	0.0307	-0.0829	-0.0089	-0.008	19.881	-5.616	18.626
9	1.8185	-0.7937	-0.0172	2.1563	0.1903	2.6598	-0.085	0.0429	-0.1414	-0.0807	0.0023	0.0294	0.2208	-0.1759	0.0827	-0.0722	-0.0489	0.0222	-0.1033	-0.0369	-0.0973	8.678	2.902	10.613
10	1.0402	-0.0044	-0.2158	1.7916	0.6169	2.2876	-0.0243	0.1194	0.0355	0.03	0.0158	-0.1285	0.1356	-0.088	0.0085	-0.1233	-0.0222	0.0116	-0.0894	-0.0256	-0.0838	10.671	11.179	6.924
11	2.5086	0.3284	-0.7194	6.4059	-6.8942	16.184	0.0194	0.0299	0.2383	0.209	0.2219	0.1324	-0.4355	-0.3821	-0.2413	-0.1241	0.0035	-0.011	-0.046	-0.0571	-0.0717	3.436	16.217	12.026
12	0.9007	0.9557	-1.101	2.6007	-1.7388	2.4759	-0.148	0.2664	0.0478	-0.3966	0.1507	-0.2216	0.1383	-0.2189	-0.0027	-0.0393	-0.0229	0.0531	-0.0024	0.0029	0.0111	21.948	17.874	-7.159
13	1.39	1.202	-1.7832	2.8095	-2.2914	3.8529	-0.0462	0.2185	0.0986	-0.1849	0.0226	-0.2253	-0.0485	-0.0116	0.0236	-0.1071	-0.0098	0.0429	-0.0482	0.0087	0.0557	26.924	18.16	-2.892
14	1.2307	-0.5937	-0.5764	2.9157	0.0672	2.2288	-0.0645	0.0053	-0.0193	0.0922	0.005	-0.0968	0.2184	-0.1377	0.0595	-0.1221	-0.0201	0.0035	-0.0974	-0.0287	-0.1169	11.362	7.968	9.77
15	0.984	0.7125	0.3989	7.5802	1.8704	2.7373	-0.0573	0.0727	0.0647	0.0909	0.0099	-0.0787	0.0524	0.0216	0.0474	-0.1531	-0.0096	0.0292	-0.0955	-0.0157	-0.0497	17.314	14.221	5.249
16	13.0306	-7.2361	1.2626	8.9938	0.1375	10.6663	-0.0251	-0.4959	0.5981	0.3942	0.6311	-1.2331	-0.1049	1.214	-0.6061	-0.0762	-0.0034	-0.0441	0.1486	-0.1767	0.0775	72.351	23.133	20.258
17	16.8053	-3.8045	2.8422	4.9016	0.1745	5.5978	0.0163	0.0728	0.3274	-0.0837	0.0792	-0.2465	-0.1761	0.0447	-0.0956	-0.0696	-0.0112	0.0472	-0.0759	-0.0253	-0.1879	59.208	25.085	14.149
18	1.628	-0.7146	-1.5003	2.4058	1.5066	2.4637	-0.0218	0.1015	0.0056	-0.0205	-0.051	0.0291	0.0295	-0.0711	0.0728	-0.0924	-0.0141	-0.0062	-0.0277	-0.0373	-0.1733	59.264	16.671	11.014
19	6.1247	-1.1325	-0.1224	4.051	2.5876	11.8097	0.1829	0.0231	0.6806	-0.2195	0.1592	-0.4826	-0.8506	1.0376	-0.3421	-0.0151	-0.0666	0.0794	0.0397	-0.0515	0.0223	70.402	22.828	10.15
20	13.3729	1.2781	-4.7796	5.0629	2.1703	4.5182	-0.1696	0.7041	-0.0493	0.1119	0.552	-0.7916	0.4097	0.7448	-0.3824	-0.1086	0.0562	-0.0447	0.2142	-0.1659	0.0217	75.329	15.335	16.115
21	5.5853	-0.5526	-4.7583	5.1031	0.3203	26.6636	-0.0484	-0.5897	-0.0101	0.412	0.0989	-0.0841	1.3145	1.126	-0.0505	0.2047	0.1319	-0.1313	0.1623	-0.0196	-0.0046	69.363	13.006	29.249
22	1.2404	-0.0223	-1.1609	0.7368	1.054	5.3343	-0.287	0.0349	-0.4374	0.5102	-0.0194	-0.2187	0.9198	0.1841	0.3064	0.2004	0.0667	0.03	0.0036	-0.0279	-0.0047	65.924	1.271	16.717
23	3.9731	0.5567	-0.8219	2.7557	0.8412	3.1038	-0.3839	-0.0881	-0.6262	0.3686	0.0438	0.0511	0.8381	0.0878	0.34	0.2099	0.0238	0.1097	-0.0405	-0.0317	0.0268	63.266	-2.425	13.93
24	9.2709	-1.6027	-4.4602	5.0634	3.6419	11.696	-0.3835	0.5735	-0.7965	0.5813	-0.2517	0.3706	0.8417	-0.8182	0.6352	0.1482	-0.1417	0.1672	-0.038	-0.1027	0.0288	51.381	1.708	18.089
25	1.9035	-1.8323	-3.1017	3.5518	3.838	6.6878	-0.3123	0.0267	-0.2383	0.5851	-0.0331	0.0675	0.8209	-0.1389	0.3453	0.0502	-0.0481	0.0578	-0.0358	-0.0218	-0.1471	55.162	10.356	23.937
26	1.174	0.333	-0.1516	1.3534	-0.7222	1.3023	0.1543	-0.1571	0.1777	0.2125	-0.0742	0.1409	-0.0407	-0.0361	-0.0801	-0.0012	-0.0278	0.0712	-0.0315	-0.0644	-0.1464	40.914	30.502	31.267
27	2.5244	-0.7397	1.2886	2.7937	-0.8175	2.4216	0.1226	-0.1552	0.0254	0.2183	-0.0392	0.1943	0.1782	-0.0564	-0.0834	-0.0333	-0.0339	0.0382	-0.0624	-0.0406	-0.1739	50.096	28.599	26.964
28	3.2257	-0.4783	-3.0353	4.2026	2.9159	10.9302	0.2685	-0.2005	0.1671	0.2985	-0.034	-0.2875	0.0267	0.3455	-0.2346	-0.0139	-0.0583	0.0027	-0.0634	0.0058	-0.1463	57.496	35.423	25.584
29	1.7165	-0.7959	-1.7511	1.3176	1.2278	2.3962	-0.063	0.1762	-0.1455	0.1559	-0.1243	0.08	0.157	-0.1624	0.1873	-0.0714	-0.0282	0.0387	-0.0188	-0.0587	-0.1659	54	14.531	14.412
30	3.4219	-1.3876	0.036	2.1158	0.2026	1.1231	0.0071	-0.0365	0.0467	0.2546	-0.0422	0.0503	0.0948	0.0052	0.0351	-0.0567	-0.0318	0.0242	-0.0595	-0.0178	-0.1801	50.65	24.881	24.642

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 12
2	X-RAY DIFFRACTION	2	A	13 - 55
3	X-RAY DIFFRACTION	3	A	56 - 80
4	X-RAY DIFFRACTION	4	A	81 - 92
5	X-RAY DIFFRACTION	5	A	93 - 120
6	X-RAY DIFFRACTION	6	A	121 - 151
7	X-RAY DIFFRACTION	7	A	152 - 181
8	X-RAY DIFFRACTION	8	A	182 - 188
9	X-RAY DIFFRACTION	9	A	189 - 223
10	X-RAY DIFFRACTION	10	A	224 - 253
11	X-RAY DIFFRACTION	11	A	254 - 267
12	X-RAY DIFFRACTION	12	A	268 - 306
13	X-RAY DIFFRACTION	13	A	307 - 346
14	X-RAY DIFFRACTION	14	A	347 - 363
15	X-RAY DIFFRACTION	15	A	364 - 377
16	X-RAY DIFFRACTION	16	B	2 - 10
17	X-RAY DIFFRACTION	17	B	11 - 20
18	X-RAY DIFFRACTION	18	B	21 - 55
19	X-RAY DIFFRACTION	19	B	56 - 67
20	X-RAY DIFFRACTION	20	B	68 - 77
21	X-RAY DIFFRACTION	21	B	78 - 88
22	X-RAY DIFFRACTION	22	B	89 - 108
23	X-RAY DIFFRACTION	23	B	109 - 140
24	X-RAY DIFFRACTION	24	B	141 - 159
25	X-RAY DIFFRACTION	25	B	160 - 180
26	X-RAY DIFFRACTION	26	B	181 - 223
27	X-RAY DIFFRACTION	27	B	224 - 248
28	X-RAY DIFFRACTION	28	B	249 - 266
29	X-RAY DIFFRACTION	29	B	267 - 350
30	X-RAY DIFFRACTION	30	B	351 - 377

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